[ensembl-dev] VEP 86 GRCh38 - alt contig names not recognized

MEYNERT Alison alison.meynert at igmm.ed.ac.uk
Mon Nov 21 15:53:09 GMT 2016


I've been annotating some GRCh38 (hs38DH) VCFs with VEP 86, and it's working fine for the primary assembly, but I'm getting warnings on the alt contig names, e.g.


WARNING: Chromosome Un_GL000218v1 not found in cache on line 3416412

It looks like VEP is just chopping the 'chr' prefixes and not fully mapping the alt contig names to the Ensembl-style versions. Both the web interface and the standalone Perl script give the same results; however, interestingly, when I enter a variant like this into the web interface, e.g.


chrUn_GL000218v1 160424 . C CTTT,CTTTT

And run the "instant VEP", I get a result (see attached screenshot). If I fix the contig name manually to GL000218.1, I get full results.

Cheers,
Alison

--
Alison Meynert
alison.meynert at igmm.ed.ac.uk

MRC Human Genetics Unit
MRC IGMM
University of Edinburgh
Western General Hospital
Crewe Road, Edinburgh EH4 2XU
United Kingdom
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